- Chimera-users - RBVI Mailing Lists

Docking
by Greta Hodo 10 Feb '20

10 Feb '20

Hi, I have a problem with the result of autodock Vina. When I load a molecule in “mol2” format and I use AutoDock Vina for docking, the docked molecule is altered. How can be possible? How can I solve my problem? I attach the photo of the real molecule [cid:C2748141-718F-40C4-8964-A212C52FDB1A] And this I how the molecule changes after the docking [cid:C1EDE285-2873-437D-A034-5BB2D031BD67] The 5-term ring becomes aromatic, while it should have only a double bond. ( this happens both if I save autodock vina result in “mol2” format and “pdb” format Hope you can help me!

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S1-8
by 林联云 10 Feb '20

10 Feb '20

Dear management， I am a PHD student from Tianjin University in china. I saw a movie which is done in chimera (see the attachment), i saw they draw a circle around the text (NTD-A). i am very confuse that i do not know how to draw a shape in chimera. i ask for you that tell me how to draw a shape in command line. Thanks very much. Best wishes, Lin l

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Re: [Chimera-users] [chimerax-users] Reproduce exact view
by Tom Goddard 10 Feb '20

10 Feb '20

Hi Elaine, Alexis, You can change a model number by command. So if you replace model #3 with model #8 that you align to #3, then delete #3, then "rename #8 id #3" will change the model id of #8 to be #3. For the step of aligning #8 to #3, if they are aligned already then #8 would open aligned to #3 unless you had moved #3 in which case you could use "view position #8 sameAs #3". Of course if the new model has not been aligned to the old you may need to use the matchmaker command to align them. Tom > On Feb 10, 2020, at 1:44 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Alexis, > We removed the forward-compatibility warning during session saving a while ago, so as long as the version you’re using is not too old, we expect the session files to be forward compatible. Still, I understand a reluctance to rely on them completely when it can take many hours or even days to set up everything the way you want. > > Sometimes I just save the session now. However, sometimes I use a “belt and suspenders” approach by saving not just the session but also a command file that has just about everything I’d used for the setup except for interactive manual positioning. I often include such a script when I add a “feature highlight” to the ChimeraX website. > > I too have often wished for an easy way to replace one model in an existing session with another. Getting the matrices (view matrix), swapping out the model, and then reapplying the matrix may be the most exact way if the models are in the same coordinate system as each other. Otherwise you could open the new model, match or fit it to the one you wish to replace, then close the one you want to get rid of. That leaves you with different model numbers, however, so if it is important to get them the same you’d have to open the new model again, match it to itself, and remove the extra intermediate copy you’d opened first. (Ugh.) > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Feb 10, 2020, at 1:22 PM, Alexis Rohou <a.rohou(a)gmail.com> wrote: >> >> Thanks Elaine, >> >> I should have added some explanation for my workflow: >> 1. I read a while back that ChimeraX sessions may or may not be forward compatible, and I wanted to ensure long-term reproducibility of my figures >> 2. a requirement I have is that I should be able to quickly remake the exact same figure after I change the input files. For example, perhaps I prototype an elaborate figure using a PDB that's a work in progress and later re-make it with an updated PDB. The advantage of a .cxc script is that I just have to change the filename near the beginning of the script and everything else stays the same. I can regenerate all my figures pretty quickly that way. That's the big payoff for investing the time to write a script upfront. >> >> The view functionality does sound very nice though, especially since I don't currently have a way to achieve transitions with my scripts (other than perhaps creating views within the scripts themselves?). Elaine, is there a way to use sessions so that I could replace a model or map with a new version of a file after I've already created a session? >> >> Cheers, >> Alexis >> >> On Mon, Feb 10, 2020 at 9:26 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> Hello, >> Maybe I’m missing something, but the “view” command allows saving and restoring named views. These are included in saved session files. I agree window size is also a factor, so you would make sure to set the same window size too. >> >> E.g. once you have the view you like then use a command like: >> >> view name myview >> >> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> >> >> Then you can save the session file and/or move things around. Later in the same session or after restoring the previously saved session from file, >> >> view myview >> >> …will restore that view. Restoring the session restores window size if you have that Window Preference set: >> <http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#window> >> >> or you could have noted the window size when you saved the view: >> >> windowsize >> >> …and then use the reported values later to restore that size, e.g. >> >> windowsize 600 400 >> >> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/windowsize.html> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >>> On Feb 10, 2020, at 8:53 AM, Alexis Rohou <a.rohou(a)gmail.com> wrote: >>> >>> Hi Christophe, >>> >>> I prepare my figures using ChimeraX command (.cxc) scripts and I believe I have a workflow that lets me reproduce exact views. I know it's not 100% robust, but it's reliable enough for me. It basically relies on a sequence of close; windowsize; view matrix; zoom; clip; save. >>> >>> Here is a pseudo script. To work out the values you need for the matrices, just move your point of view and your models until you are happy, then do "view matrix". I have not worked out a good way to get the distances for the clip planes. So I just play with them on the command line until I get the look I want, then save the values in my cxc file. >>> >>> Hope this helps & that more experienced users can chime in with improvements. >>> >>> Cheers, >>> Alexis >>> >>> >>> # close anything currently open >>> close >>> # go to relevant directory >>> cd /my/absolute/path >>> # >>> windowsize 1200 1200 >>> camera ortho >>> clip near off far off front off back off >>> # Open files >>> open my_model.pdb name "my model" >>> open my_map.mrc name "my map" >>> # etc. >>> >>> #insert here coloring, styles, for the model/map/background etc >>> >>> # Go to your favorite view point, save a shot >>> view matrix camera 1,0,0,182.59,0,1,0,229.79,0,0,1,352.89 >>> zoom 0.33 >>> clip near off far off front off back off; clip near -100.0 far +100.0 front off back off >>> ~select >>> save my_figure.png supersample 3 transparentBackground false >>> >>> # If you need to move your models >>> view matrix models #1,0.91269,-0.0093359,-0.40855,59.153,-0.40865,-0.018906,-0.91249,368.7,0.00079806,0.99977,-0.02107,-44.893,#2,-0.83654,-0.058918,-0.54474,344.52,-0.54355,-0.035951,0.83861,293.33,-0.068993,0.99762,-0.0019503,-42.032 >>> >>> # then take another shot >>> view matrix camera 0.98289,-0.005269,-0.18408,131.07,-0.17421,-0.3506,-0.92018,70.662,-0.059691,0.93651,-0.34553,163.8 >>> clip near off far off front off back off; clip near -20.0 far +12.0 front off back off >>> save Figures/TRPA1_3551_binding_site_details1.png supersample 3 transparentBackground false >>> >>> >>> >>> >>> On Sun, Feb 9, 2020 at 10:01 AM Christophe Leterrier <christophe.leterrier(a)gmail.com> wrote: >>> Hi, >>> >>> I haven't been able to find how to >>> - log >>> - set >>> - store >>> - recall >>> >>> a precise view (ie get the same exact image if I do a snapshot). >>> >>> First use case would within the same session (fixed computer, window size, no restart of the application in between). Second use case (more tricky?) would be independently of computer / window size / current session. >>> >>> Thanks for your help! >>> >>> Christophe >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users > > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu > Manage subscription: > http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users >

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moving parts of a density map in a Movie
by Sen, Anindito 05 Feb '20

05 Feb '20

Dear All, I have a composite density map with 7 individual reconstructions combined together. For making a movie to show the different components and their organization- What will be the commands to make the individual density maps to move out of their position (in the composite map) and fly back in, (one or multiple density maps at a time). Regards Anindito Sen. Ph.D

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Phosphorylated residues showing up as X
by Daniel Hilger 05 Feb '20

05 Feb '20

Hi, I modeled two phosphorylated residues in my structure. The primary sequence window in Chimera, however, is only showing a “X” at those positions. Is there a possibility to change that to the original amino acid (S or T) or to show them as SEP or TPO in the sequence window? Thanks, Daniel Daniel Hilger, Dr. Group leader Philipps-University Marburg Marbacher Weg 6 35032 Marburg Germany daniel.hilger(a)pharmazie.uni-marburg.de Phone: +49 6421 28 25930

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Chimera Download issue
by Zachary Maldonado 04 Feb '20

04 Feb '20

To whom it may concern, My name is Zachary Maldonado and I am a college student at the University of Missouri-Columbia. I need this program for one of my classes I am taking this semester. I can not seem to open the program and when I try to open it, I get a message from my computer saying that I need to update the application before I can open it. My computer says it is unable to search for "malicious software". If you could assist me that would be greatly appreciated. Thank you! Sincerely, Zachary Maldonado

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Supporting XDG base directory - chimera
by Martín González Buitrón 04 Feb '20

04 Feb '20

Dears all, I realised that you are using a hidden folder (.chimera/) in $HOME directory, linux's distribution. Have you considered supporting freedesktop.org's standard specs? References: - http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html - https://wiki.archlinux.org/index.php/XDG_Base_Directory All the best, Martín

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MD chimera bug
by Fabian Glaser 31 Jan '20

31 Jan '20

Dear Chimera developers, I think I have found abug in the MD movies tool in Chimera, when trying to use the Per-Frame command Script: When selecting residues > :1000 (which have a residue number > 1000) it does not select the the residue, since it adds to the residue number the frame number, for example see the figure attached, with this logic, and trying to apply the script, if the I try to select residue :1000 the script gives a mistake and this is because it tries to select residue frame + residue number (in this case 96000) which of course does not exist. The same sequence works perfectly if the selection is done outside the script Best, Fabian Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ <https://lokey.technion.ac.il/bioinformatic-knowledge-unit/> Tel +972 (0) 4 8293701

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conjugate moiety to protein PDB
by Michael Scott Bowers 30 Jan '20

30 Jan '20

Hi power users, I have 2 tasks that I hope you can help with. Both of these require conjugation of a moiety to multiple places on a large, multi chain protein. Command line solutions are fine. Task 1. Conjugate some group like a tosyl to selected cystine residues. There could be about 200 residues needing conjugation across 4 chains of a protein PDB file. Task 2. Conjugate a peptide chain to the N or C terminus of a multi chain protein PDB file. I am already familiar with build structure protein and smiles, but connecting models without severe steric hindrance is problematic. Also, given the number of needed conjugations, it would be great it I could do this via command line (or some other function that I am currently not aware of) so that the tosyl or peptide chains needing connecting do not have to be positioned prior to making the covalent bond. Much thanks to everyone in advance. Best, Scott

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Auto-associate define attribute/render by attribute
by Healey, Joseph 24 Jan '20

24 Jan '20

Hi Chimera team, I’m working on a script to automatically render proteins in a complex by attributes (in this case, a number of scores obtained from different immunogenicity prediction algorithms). I currently have the script outputting attribute files as intended, but ideally I’d like to define the same attributes across all the chains of the model, which are made up of a number of different proteins. Is there any way for me to define the attribute file, or utilise some functionality to auto-associate an attribute file with all of the chains which have the correct sequence (similarly to how the sequence alignment input works at the moment?). Currently the attribute file is only using ‘numbered’ coordinates (:1, :2, :3…etc) , rather than the actual sequence. Since there’s no chain information in the attribute files, I’m not sure how I can go about connecting it to the right structure, other than manually at the moment? Many thanks, Joe Dr. Joseph Healey Ph.D. M.Sc. B.Sc. (Hons) MRSB Research Fellow Warwick Medical School University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> Email: J.Healey.1(a)warwick.ac.uk<mailto:J.Healey.1@warwick.ac.uk> | ORCID: orcid.org/0000-0002-9569-6738

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